Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttctacaactctttttgtctcctttcaaacagtttacatagactctcattataagccatgatctgtcattacttgagtcaatctctctctgtttattagtgattaaagttgtatagtgactatgctagcatttacctaccttgtcgttattaagtgatatatgtggtgccgttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTCAAGGAAGAAACTGTCGAATATGTTTTGGCTTTGATTTATGAAATGCTCT

Basic information

species Arabidopsis thaliana
transcript AT3G42050.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G42050.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv16s0039g01610.t01 (Vitis vinifera), 3'ss of exon 2
gtaagttttctacaactctttttgtctcctttcaaacagtttacatagactctcattataagccatgatctgtcattacttgagtcaatctctctctgtttattagtgattaaagttgtatagtgactatgctagcatttacctaccttgtcgttattaagtgatatatgtggtgccgttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTCAAGGAAGAAACTGTCGAATATGTTTTGGCTTTGATTTATGAAATGCTCT
                                                                                | | |     | |   ||   | |  |   ||  |  |||||   |  |  || | |  | | |     || | |||| | |   | | |  | | |  | |  ||||||||||| |||||||||    | ||||| ||||| |||||||||||||||||||||||||| || ||||||||  ||||  ||||| ||||||||||  
--------------------------------------------------------------------------------taactaggattatagttgagaactgttctgtattggagtataagaatgagccttgtaaatgctt--taagttgatattgact---agaggaagcgtc--tgtgacagGATGGTCCTGCTTATGTTAGGGTGTTTGTGAGCATTTTACGTGATATATTCAAGGAAGAAACAGTTGAATATGTGCTGGCACTGATTGATGAAATGCTAA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|47832017|gb|CK121701.1|CK121701
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|86031310|gb|DR327063.1|DR327063
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|116433606|gb|EG476198.1|EG476198
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|116433595|gb|EG476187.1|EG476187
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|86031298|gb|DR327051.1|DR327051
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|86031307|gb|DR327060.1|DR327060
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|86031303|gb|DR327056.1|DR327056
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|86031311|gb|DR327064.1|DR327064
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|86031308|gb|DR327061.1|DR327061
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|86031304|gb|DR327057.1|DR327057
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|86031313|gb|DR327066.1|DR327066
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTAAGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|86031315|gb|DR327068.1|DR327068
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|86031316|gb|DR327069.1|DR327069
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|86031312|gb|DR327065.1|DR327065
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|86031300|gb|DR327053.1|DR327053
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGAACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|124798956|gb|EH888635.1|EH888635
EST:     CGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGAT
genomic: CGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGAT
EST: gi|86031317|gb|DR327070.1|DR327070
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGAACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTC
EST: gi|124726092|gb|EH817494.1|EH817494
EST:     GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAA                         GATGGTCCAGCTTATGTTCATCTCT
genomic: GGCGCTATGATAAAAAACCTGAAAGTGCTAGGGCACAGTTGCTCGATGAAgtaagttttc ... gttattgcagGATGGTCCAGCTTATGTTCATCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcatttacctaccttgtcgttattaagtgatatatgtggtgccgttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTCAAGGAAGAAACTGTCGAATATGTTTTGGCTTTGATTTATGAAATGCTCT
                     ttattaagtgatatat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttctacaactctttttgtctcctttcaaacagtttacatagactctcattataagccatgatctgtcattacttgagtcaatctctctctgtttattagtgattaaagttgtatagtgactatgctagcatttacctaccttgtcgttattaagtgatatatgtggtgccgttattgcagGATGGTCCAGCTTATGTTCATCTCTTTGTTAGCATCTTACGTGATATATTCAAGGAAGAAACTGTCGAATATGTTTTGGCTTTGATTTATGAAATGCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA